+

WO2024107624A1 - Méthodes permettant de surmonter la résistance à des thérapies par inhibiteur de point de contrôle - Google Patents

Méthodes permettant de surmonter la résistance à des thérapies par inhibiteur de point de contrôle Download PDF

Info

Publication number
WO2024107624A1
WO2024107624A1 PCT/US2023/079476 US2023079476W WO2024107624A1 WO 2024107624 A1 WO2024107624 A1 WO 2024107624A1 US 2023079476 W US2023079476 W US 2023079476W WO 2024107624 A1 WO2024107624 A1 WO 2024107624A1
Authority
WO
WIPO (PCT)
Prior art keywords
inhibitor
cancer
limited
therapy
cells
Prior art date
Application number
PCT/US2023/079476
Other languages
English (en)
Inventor
Taylor Schreiber
George FROMM
Suresh DE SILVA
Original Assignee
Shattuck Labs, Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Shattuck Labs, Inc. filed Critical Shattuck Labs, Inc.
Publication of WO2024107624A1 publication Critical patent/WO2024107624A1/fr

Links

Classifications

    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/04—Antineoplastic agents specific for metastasis
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K67/00—Rearing or breeding animals, not otherwise provided for; New or modified breeds of animals
    • A01K67/027—New or modified breeds of vertebrates
    • A01K67/0271—Chimeric vertebrates, e.g. comprising exogenous cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • G01N33/57488—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites involving compounds identifable in body fluids
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • G01N33/57492—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites involving compounds localized on the membrane of tumor or cancer cells
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2207/00—Modified animals
    • A01K2207/12—Animals modified by administration of exogenous cells
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2207/00—Modified animals
    • A01K2207/15—Humanized animals
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2227/00—Animals characterised by species
    • A01K2227/10—Mammal
    • A01K2227/105—Murine
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2267/00—Animals characterised by purpose
    • A01K2267/03—Animal model, e.g. for test or diseases
    • A01K2267/0331—Animal model for proliferative diseases
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Definitions

  • the present disclosure relates to, in part, methods that are useful for detection and treatment of drug resistant cancer, and methods for developing new therapeutics against drug resistant cancers.
  • Drug resistance remains one of the biggest challenges in cancer therapy. Drug resistance is found across all types of cancer and all modes of treatment, including molecularly targeted therapy, immunotherapy, and chemotherapy. It is also common that a patient with advanced cancer receives a drug that is efficacious, but then weeks or months later the cancer recurs, and drug efficacy is lost or reduced. Unfortunately, few effective therapeutic options are available for patients having cancers that are resistant to the anti-checkpoint therapies. Developmentof resistance to checkpoint therapy appears to depend on genetic and immunological background of the host. For example, diverse types of effector T cells, which play a role in eliminating cancers, compete with Tregs in the tumor environment, which suppress not only the native anticancer immunity as well as the efficacy of immune checkpoint inhibitors.
  • CD4+CD25+ T regulatory cells contribute to resistance to anti-PD-1 therapeutics.
  • Kamada et al. PD-1 + regulatory T cells amplified by PD-1 blockade promote hyperprogression of cancer, Proc. Natl. Acad. Sci. USA 2019; 116 (20) 9999-10008; Zuazo et al., Systemic CD4 Immunity as a Key Contributor to PD-L1/PD-1 Blockade Immunotherapy Efficacy, Front Immunol.
  • NK cells also appear to have a function in resistance to checkpoint inhibitors.
  • p53 which is the most frequently mutated tumor suppressor in human cancers, plays a role in both regulation of immunity and developing resistance to anti-checkpoint therapy.
  • Shi and Jiang A Different Facet of p53 Function: Regulation of Immunity and Inflammation During Tumor Development, Front Cell Dev B/o/ 2021 ; 9:762651 ; Wang eta/., Epithelial Mutant p53 Promotes Resistance to Anti-PD-1 -Mediated Oral Cancer Immunoprevention in Carcinogen-Induced Mouse Models, Cancers (Basel) 2021; 13(6): 1471 ; Sobol etal., Effect of adenoviral p53 (Ad-p53) tumor suppressor immune gene therapy on checkpoint inhibitor resistance and abscopal therapeutic efficacy.
  • the present disclosure provides, in part, methods for selecting patients having a potent NK-cell mediated cytotoxicity, a Th1 - and/or M1 -dominant immune response, and/or weak activity of CD4- ⁇ D25+T regulatory cells and/or patients suffering from a p53 mutant cancer, which is or is at risk of being checkpoint resistant, for cancer treatment, and methods for cancer treatment, based on, for instance, based on gene expression profiles of anti-PD-1 resistant cancers, he present disclosure also provides animal models suitable for testing an anti-cancer drug candidate for treating a p53 mutant cancer, which is or is at risk of being checkpoint resistant, and methods for making a pharmaceutical composition for treating cancer.
  • the present disclosure relates to a method for selecting for a cancer treatment a patient having higher activity of Tregs compared to effector T cells in the tumor microenvironment, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of treating a cancer in a patient having higher activity of Tregs compared to effector T cells in the tumor microenvironment, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of determining treatment for a cancer in a subject that exhibits a potent NK-cell mediated cytotoxicity, a Th1- and/or M1-dominant immune response, and/or weak activity of CD4- ⁇ D25+T regulatory cells: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method for selecting for a cancer treatment in a subject for cancer treatment, wherein the subject exhibits a potent NK-cell mediated cytotoxicity, a Th1- and/or M1- dominant immune response, and/or weak activity of CD4+CD25+T regulatory cells, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of treating a cancer in a subject that exhibits a potent NK-cell mediated cytotoxicity, a Th1- and/or M1 -dominant immune response, and/or weak activity of CD4-HDD25+T regulatory cells, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the presence of the potent NK-cell mediated cytotoxicity is determined based on measurement of one or more of the proportion of NKP46+ cells, the proportion of NKP46+CD69+ cells, extent of CD107a surface expression, extent of cytokine production (e.g. production of one or more of IFNy NFa, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1, CCL2, CCL3, CCL4, CCL5, and CXCL8), and extent of lysis of target cells.
  • GM-CSF granulocyte macrophage colony-stimulating factor
  • the presence of the Th 1 - and/or M1 -dominant immune response compared to a control is determined based on one or more of the ratios of IgMJgG and/or IgEJgG antibodies, extent of cytokine production (e.g., production of one or more of IFNy, TNFa, LTa, IL- 17A, IL-6, IL-12, CXCR3, CCR5), surface expression of one or more markers (e.g., iNOS, CD80, CD86, CD64, CD16 and CD32, along with CD68 and/or CD11 b).
  • cytokine production e.g., production of one or more of IFNy, TNFa, LTa, IL- 17A, IL-6, IL-12, CXCR3, CCR5
  • markers e.g., iNOS, CD80, CD86, CD64, CD16 and CD32, along with CD68 and/or CD11 b).
  • the presence of the weak activity of CD4-HDD25+T regulatory cells compared to a control is determined based on one or more of the proportion of CD4+CD25+T regulatory cells in peripheral blood, extent of cytokine production (e.g., production of IL-2, IL-10 and TGF0), proliferation assay.
  • the control is selected from a standard value or a sample from one or more normal subjects, subjects suffering from cancer, subjects suffering from cancer relapse, or a combination thereof.
  • the present disclosure relates to a method of determining treatment for a p53 mutant cancer in a patient, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method for selecting a patient having a p53 mutant cancer for a cancer treatment, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of treating a p53 mutant cancer, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is selected.
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is selected.
  • a lack of upregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation is observed compared to a prior biological sample obtained from the subject a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1, PD-L1 and/or PD-L2 is selected.
  • a cancer monotherapy when an upregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation is observed compared to a healthy tissue, a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1, PD-L1 and/or PD-L2 is not selected.
  • a chemotherapy is selected, the chemotherapy is selected from an antimetabolite chemotherapeutic (e.g., 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo- L-norleucine (DON), azaserine and acivicin), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc.); and a protein translation inhibitor (e.g., silvestrol and omacetaxine), a ribosome biogenesis inhibitor (e.g., diazaborine, lamotrigine and ribozinoindoles), an inhibitor of rRNA and/or tRNA synthesis (e.g., quarfloxin (CX-3543) and CX-5461), an inhibitor of synthesis of amino acids (e.g., GLUD1 inhibitor R162, BCAT1 inhibitor gaba
  • the chemotherapy is selected in combination with a cancer therapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2.
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is not selected.
  • a chemotherapy is selected, the chemotherapy is selected from an antimetabolite chemotherapeutic (e.g., 5- fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo-L-norleucine (DON), azaserine and acivicin), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc.); and a protein translation inhibitor (e.g., silvestrol and omacetaxine), a ribosome biogenesis inhibitor (e.g., diazaborine, lamotrigine and ribozinoindoles), an inhibitor of rRNA and/or tRNA synthesis (e.g., quarfloxin (CX-3543) and CX-5461), an inhibitor of synthesis of amino acids (e.g., GLUD1 inhibitor R162, BCAT1 inhibitor gaba
  • the chemotherapy is selected in combination with a cancer therapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2.
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is not selected.
  • a chemotherapy is selected, the chemotherapy is selected from an antimetabolite chemotherapeutic (e.g, 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo-L-norleucine (DON), azaserine and acivicin), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc.); and a protein translation inhibitor (e.g., silvestrol and omacetaxine), a ribosome biogenesis inhibitor (e.g., diazaborine, lamotrigine and ribozinoindoles), an inhibitor of rRNA and/or tRNA synthesis (e.g., quarfloxin (CX-3543) and CX-5461), an inhibitor of synthesis of amino acids (e.g., GLUD1 inhibitor R162, BCAT1 inhibitor gabap
  • the one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation is selected from Statl, Stat2, Tapi , Ifitm2, and Ifitm3.
  • the present disclosure relates to a method of determining treatment for a cancer in a subject that exhibits a potent NK-cell mediated cytotoxicity, a Th1 - and/or M1-dominant immune response, and/or weak activity of CD4+CD25+T regulatory cells: (a) contacting a cultured biological sample from a subject with IFNy for less than about 8 hours; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method for selecting for a cancer treatment in a subject for cancer treatment, wherein the subject exhibits a potent NK-cell mediated cytotoxicity, a Th1 - and/or Mi- dominant immune response, and/or weak activity of CD4+CD25+T regulatory cells, the method comprising: (a) contacting a cultured biological sample from a subject with IFNy for less than about 8 hours; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of treating a cancer in a subject that exhibits a potent NK-cell mediated cytotoxicity, a Th1- and/or M1 -dominant immune response, and/or weak activity of CD4-RDD25+ T regulatory cells, the method comprising: (a) contacting a cultured biological sample from a subject with I FNy for less than about 8 hours; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of determining treatment for a p53 mutant cancer in a patient, the method comprising: (a) contacting a cultured biological sample from a subject with IFNy for less than about 8 hours; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the presence of the potent NK-cell mediated cytotoxicity is determined based on measurement of one or more of the proportion of NKP46+ cells, the proportion of NKP46CD69+ cells, extent of CD107a surface expression, extent of cytokine production (e.g. production of one or more of IFNy NFo, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1, CCL2, CCL3, CCL4, CCL5, and CXCL8), and extent of lysis of target cells.
  • GM-CSF granulocyte macrophage colony-stimulating factor
  • the presence of the Th 1 - and/or M1 -dominant immune response compared to a control is determined based on one or more of the ratios of IgM :lgG and/or IgEJgG antibodies, extent of cytokine production (e.g., production of one or more of IFNy, TNFa, LTa, IL- 17A, IL-6, IL-12, CXCR3, CCR5), surface expression of one or more markers (e.g., iNOS, CD80, CD86, CD64, CD16 and CD32, along with CD68 and/or CD11 b).
  • cytokine production e.g., production of one or more of IFNy, TNFa, LTa, IL- 17A, IL-6, IL-12, CXCR3, CCR5
  • markers e.g., iNOS, CD80, CD86, CD64, CD16 and CD32, along with CD68 and/or CD11 b).
  • the presence of the weak activity of CD4+CD25+T regulatory cells compared to a control is determined based on one or more of the proportion of CD4+CD25+T regulatory cells in peripheral blood, extent of cytokine production (e.g., production of IL-2, IL-10 and TGFP), proliferation assay.
  • the control is selected from a standard value or a sample from one or more normal subjects, subjects suffering from cancer, subjects suffering from cancer relapse, or a combination thereof.
  • the present disclosure relates to a method for selecting a patient having a p53 mutant cancer for a cancer treatment, the method comprising: (a) contacting a cultured biological sample from a subject with IFNy for less than about 8 hours; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of treating a p53 mutant cancer, the method comprising: (a) contacting a cultured biological sample from a subject with IFNy for less than about 8 hours; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the cultured biological sample from a subject is contacted with an interferon for less than about 7 hr, or less than about 6 hr, or less than about 5 hr, or less than about 4 hr, or less than about 3 hr, or less than about 2 hr, or less than about 1 hr. In embodiments, the cultured biological sample from a subject is contacted with an interferon for at least about 5 minutes, or at least about 10 minutes, or at least about 15 minutes, or at least about 30 minutes, or at least about 45 hr, or at least about 1 hr, or at least about 2 hr, or at least about 3 hr, or at least about 4 hr.
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is selected.
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is selected.
  • an upregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation is observed compared to a prior biological sample obtained from the subject, a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1, PD-L1 and/or PD-L2 is selected.
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is not selected. Instead, in embodiments, a chemotherapy is selected.
  • the chemotherapy is selected from an antimetabolite chemotherapeutic (e.g., 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo-L-norleucine (DON), azaserine and acivicin), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc.); and a protein translation inhibitor (e.g., silvestrol and omacetaxine), a ribosome biogenesis inhibitor (e.g., diazaborine, lamotrigine and ribozinoindoles), an inhibitor of rRNA and/or tRNA synthesis (e.g., quarfloxin (CX-3543) and CX-5461), an inhibitor of synthesis of amino acids (e.g., GLUD1 inhibitor R162, BCAT1 inhibitor gabapentin, glutamina
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1, PD-L1 and/or PD-L2 is not selected. Instead, in embodiments, a chemotherapy is selected.
  • the chemotherapy is selected from an antimetabolite chemotherapeutic (e.g., 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo-L-norleucine (DON), azaserine and acivicin), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc.); and a protein translation inhibitor (e.g., silvestrol and omacetaxine), a ribosome biogenesis inhibitor (e.g., diazaborine, lamotrigine and ribozinoindoles), an inhibitor of rRNA and/or tRNA synthesis (e.g., quarfloxin (CX-3543) and CX-5461), an inhibitor of synthesis of amino acids (e.g., GLUD1 inhibitor R162, BCAT1 inhibitor gabapentin, glutamina
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1, PD-L1 and/or PD-L2 is not selected. Instead, in embodiments, a chemotherapy is selected.
  • the chemotherapy is selected from an antimetabolite chemotherapeutic (e.g., 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo- L-norleucine (DON), azaserine and acivicin), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc.); and a protein translation inhibitor (e.g., silvestrol and omacetaxine), a ribosome biogenesis inhibitor (e.g., diazaborine, lamotrigine and ribozinoindoles), an inhibitor of rRNA and/or tRNA synthesis (e.g., quarfloxin (CX-3543) and CX-5461), an inhibitor of synthesis of amino acids (e.g., GLUD1 inhibitor R162, BCAT1 inhibitor gabapentin, glutamina
  • the one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation is selected from Statl, Stat2, Tapi , Ifitm2, and Ifitm3.
  • the biological sample comprises at least one tumor cell.
  • the evaluating is performed by DNA sequencing, RNA sequencing, immunohistochemical staining, western blotting, in cell western, immunofluorescent staining, ELISA, and fluorescent activating cell sorting (FACS) or a combination thereof.
  • the evaluating informs classifying the patient into a high- or low-risk group.
  • the high-risk classification comprises a high level of tumor cells having resistance to the cancer therapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2.
  • the low- risk classification comprises a low level of tumor cells having resistance to the cancer therapy with an ability to reduce or inhibit function and/or activity of PD-1, PD-L1 and/or PD-L2.
  • the present disclosure relates to a transgenic non-human animal comprising one or more p53 mutant tumor cells, wherein the tumor cells exhibit: (a) an upregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and/or (b) a lack of significant upregulation and/or a downregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation, when contacted with IFNy for less than about 8 hours.
  • the tumor cells are resistant to a cancer therapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2.
  • the cancer therapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is an antibody.
  • the antibody is a human or humanized antibody.
  • the antibody is selected from nivolumab (OPDIVO), pembrolizumab (KEYTRUDA), pidilizumab (CT-011, CURE TECH), MK-3475 (MERCK), BMS 936559, MPDL328OA (ROCHE), Cemiplimab (LIBTAYO), Atezolizumab (TECENTRIQ), Avelumab (BAVENCIO), and Durvalumab (imfinzi).
  • OPDIVO nivolumab
  • KEYTRUDA pembrolizumab
  • pidilizumab CT-011, CURE TECH
  • MK-3475 MK-3475
  • BMS 936559 MPDL328OA
  • ROCHE Cemiplimab
  • LIBTAYO Cemiplimab
  • Atezolizumab TECENTRIQ
  • Avelumab BAVENCIO
  • Durvalumab imfinzi
  • the present disclosure relates to a method of making a transgenic non-human animal comprising one or more p53 mutant cancer cells that are nonresponsive, resistant, or recalcitrance to a cancer therapy, wherein the cancer therapy has an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2, the method comprising: (a) injecting one or more parental p53 mutant cancer cells that are responsive to the cancer therapy in a non-human animal; (b) administering the cancer therapy to the non-human animal; (c) isolating cancer cells that survive the cancer therapy; (d) injecting cancer cells that survive the cancer therapy in a different non-human animal of the same species; and (e) repeating steps (b) to (d) three to ten more times.
  • the present disclosure relates to a method of making a transgenic non-human animal comprising one or more p53 mutant cancer cells that are nonresponsive, resistant, or recalcitrance to a cancer therapy, wherein the non-human animal exhibits a potent NK-cell mediated cytotoxicity, a Th1 - and/or M1 -dominant immune response, and/or weak activity of CD4- 25+ T regulatory cells, and wherein the cancer therapy has an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2, the method comprising: (a) injecting one or more parental p53 mutant cancer cells that are responsive to the cancer therapy in a non-human animal; (b) administering the cancer therapy to the non-human animal; (c) isolating cancer cells that survive the cancer therapy; (d) injecting cancer cells that survive the cancer therapy in a different non-human animal of the same species; and (e) repeating steps (b) to (d) three to ten more
  • steps (b) to (d) are repeated at least three times more. In embodiments, steps (b) to (d) are repeated at least four times more. In embodiments, steps (b) to (d) are repeated at least five times more. In embodiments, steps (b) to (d) are repeated less than eight times.
  • the cancer cells that survive the cancer therapy grow faster than the parental p53 mutant cancer cells in the presence of the cancer therapy that has an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2.
  • the transgenic non-human animal is a rodent.
  • the rodent is a mouse.
  • the mouse belongs to BALB/c or C57BL/6 strain.
  • FIG. 1A and FIG. 1 B illustrate the generation of anti-PD-1 -resistant MC38 tumors.
  • FIG. 1A shows a schematic representation of the method used to generation of anti-PD-1-resistant MC38 tumors. The cells obtained after five rounds of selection are also referred to as MC38/AR herein.
  • FIG. 1B shows a graph comparing the efficacy of an anti-PD-1 antibody (100 pg anti-PD-1 clone RMP1-14; BioXcell) in C57BL/6 mice harboring MC38 parental cells or PD-1 resistant MC38 cells obtained after third, fourth and fifth round of selection.
  • FIG. 2E show the comparison of normalized baseline expression of the following genes in MC38/AR cells and MC38 parental cells: Statl (FIG. 2A), Stat2 (FIG. 2B), Tapi (FIG. 2C), Ifitm2 (FIG. 2D), and Ifitm3 (FIG. 2E).
  • Gene expression was quantified using qRT-PCR, expression was normalized in comparison expression of the housekeeping control gene Rsp18 using the ddCt method, the relative expression in MC38 parental cells to 1 and plotted.
  • FIG. 3A to FIG. 3E show the comparison of normalized expression of the following genes in MC38/AR cells and MC38 parental cells in the presence of I FNy: Statl (FIG. 3A), Stat2 (FIG. 3B), Tapi (FIG. 3C), Ifitm2 (FIG. 3D), and Ifitm3 (FIG. 3E).
  • Gene expression was quantified using qRT-PCR, expression was normalized in comparison expression of the housekeeping control gene Rsp18 using the ddCt method, the relative expression in MC38 parental cells to 1 and plotted.
  • the current disclosure is based, in part, the discovery of surprising upregulation in anti-PD-1 resistant cells of certain genes associated with interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation in tumors in a host that shows a potent NK-cell mediated cytotoxicity, a Th 1 - and/or M1-dominant immune response, and weak activity of CD4-CD25+T regulatory cells.
  • EZH2 inhibition activates a dsRNA-STING- interferon stress axis that potentiates response to PD-1 checkpoint blockade in prostate cancer, Nat Cancer 2021 ; 2(4):444-456; Muller et al., Type I Interferons and Natural Killer Cell Regulation in Cancer, Front Immunol. 2017; 8: 304; Mizutani et al., Conditional IFNAR1 ablation reveals distinct requirements of type I IFN signaling for NK-cell maturation and tumor surveillance.
  • the current disclosure is also based, in part, the discovery of surprising dysregulation of certain genes associated with interferon response in p53-mutant tumors. This is surprising, inter alia, because p53 is known to have a role in the interferon response. Munoz-Fontela et al., Transcriptional role of p53 in interferon- mediated antiviral immunity, J Exp Med.
  • TGF activation which is reported by Bernard et al., inhibits IFNy signaling Gabrielian et al., Effect of TGF-beta on interferon-gamma-induced HLA-DR expression in human retinal pigment epithelial cells, Invest Ophthalmol Vis Sci .
  • TGF-beta 1 inhibition of IFN-gamma-induced signaling and Th1 gene expression in CD4+ T cells is Smad3 independent but MAP kinase dependent, Mol Immunol . 2007; 44(13):3283-90.
  • Disclosed herein is an anti-PD-1 -resistant tumor model based murine colorectal carcinoma MC38 cells in C57BL/6 mice, which exbibit potent NK-cell mediated cytotoxicity, a Th1- and/or M1-dominant immune response, and weak activity of CD4+CD25+ T regulatory cells.
  • the present disclosure relates to a method of determining treatment for a cancer in a subject that exhibits a potent NK-cell mediated cytotoxicity, a Th1- and/or M1-dominant immune response, and/or weak activity of CD4+CD25+T regulatory cells: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method for selecting for a cancer treatment in a subject for cancer treatment, wherein the subject exhibits a potent NK-cell mediated cytotoxicity, a Th1- and/or M1- dominant immune response, and/or weak activity of CD4+CD25+T regulatory cells, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of treating a cancer in a subject that exhibits a potent NK-cell mediated cytotoxicity, a Th1- and/or M1 -dominant immune response, and/or weak activity of CD4-HDD25+T regulatory cells, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the presence of the potent NK-cell mediated cytotoxicity is determined based on measurement of one or more of the proportion of NKP46+ cells, the proportion of NKP46+CD69+ cells, extent of CD107a surface expression, extent of cytokine production (e.g. production of one or more of IFNy NFo, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1, CCL2, CCL3, CCL4, CCL5, and CXCL8), and extent of lysis of target cells.
  • GM-CSF granulocyte macrophage colony-stimulating factor
  • the presence of the Th 1 - and/or M1 -dominant immune response compared to a control is determined based on one or more of the ratios of IgMJgG and/or IgEJgG antibodies, extent of cytokine production (e.g., production of one or more of IFNy, TNFa, LTa, IL- 17A, IL-6, IL-12, CXCR3, CCR5), surface expression of one or more markers (e.g., iNOS, CD80, CD86, CD64, CD16 and CD32, along with CD68 and/or CD11 b).
  • cytokine production e.g., production of one or more of IFNy, TNFa, LTa, IL- 17A, IL-6, IL-12, CXCR3, CCR5
  • markers e.g., iNOS, CD80, CD86, CD64, CD16 and CD32, along with CD68 and/or CD11 b).
  • the presence of the weak activity of CD4-HDD25+T regulatory cells compared to a control is determined based on one or more of the proportion of CD4+CD25+T regulatory cells in peripheral blood, extent of cytokine production (e.g., production of IL-2, IL-10 and TGF0), proliferation assay.
  • the control is selected from a standard value or a sample from one or more normal subjects, subjects suffering from cancer, subjects suffering from cancer relapse, or a combination thereof.
  • the presence of the potent NK-cell mediated cytotoxicity is determined based on measurement of one or more of the proportion of NKP46+ cells, the proportion of NKP46+CD69+ cells, extent of CD107a surface expression, extent of cytokine production (e.g. production of one or more of IFNy, TNFa, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1, CCL2, CCL3, CCL4, CCL5, and CXCL8), and extent of lysis of target cells.
  • cytokine production e.g. production of one or more of IFNy, TNFa, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1, CCL2, CCL3, CCL4, CCL5, and CXCL8
  • the determination of a potent NK-cell mediated cytotoxicity is performed by DNA sequencing, RNA sequencing, immunohistochemical staining, western blotting, in cell western, immunofluorescent staining, ELISA, and fluorescent activating cell sorting (FACS) or a combination thereof.
  • the determination of a potent NK-cell mediated cytotoxicity is performed by contacting the sample with an agent that specifically binds to a protein selected from NKP46, CD69, IFNy, TNFa, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1 , CCL2, CCL3, CCL4, CCL5, and CXCL8.
  • the agent that specifically binds to a protein selected from NKP46, CD69, IFNy, TNFa, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1, CCL2, CCL3, CCL4, CCL5, and CXCL8 is an antibody, a binding fragment thereof, an antibody-like molecule, or a binding fragment thereof.
  • the determination of a potent NK-cell mediated cytotoxicity is performed by contacting the sample with an agent that specifically binds to one or more of nucleic acids that encodes one or more proteins selected from protein selected from NKP46, CD69, IFNy, TNFa, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1 , CCL2, CCL3, CCL4, CCL5, and CXCL8.
  • the agent that specifically binds to one or more of the nucleic acids is a nucleic acid primer or probe.
  • the presence of the Th1 - and/or M1-dominant immune response compared to a control is determined based on one or more of the ratios of IgMJgG and/or IgEJgG antibodies, extent of cytokine production (e.g., production of one or more of IFNy, TNFo, LTa, IL-17A, IL-6, IL-12, CXCR3, CCR5), surface expression of one or more markers (e.g., iNOS, CD80, CD86, CD64, CD16 and CD32, along with CD68 and/or CD11 b).
  • cytokine production e.g., production of one or more of IFNy, TNFo, LTa, IL-17A, IL-6, IL-12, CXCR3, CCR5
  • markers e.g., iNOS, CD80, CD86, CD64, CD16 and CD32, along with CD68 and/or CD11 b).
  • the determination of a presence of the Th1- and/or M1-dominant immune response is performed by DNA sequencing, RNA sequencing, immunohistochemical staining, western blotting, in cell western, immunofluorescent staining, ELISA, and fluorescent activating cell sorting (FACS) or a combination thereof.
  • the determination of a presence of the Th1 - and/or M1 -dominant immune response is performed by contacting the sample with an agent that specifically binds to a protein selected from IgM, IgG, IgE, IFNy, TNFa, LTa, IL-17A, IL-6, IL-12, CXCR3, CCR5, iNOS, CD80, CD86, CD64, CD16 and CD32, CD68, and CD11 b.
  • the agent that specifically binds to a protein selected from IgM, IgG, IgE, IFNy, TNFa, LTa, IL-17A, IL-6, IL-12, CXCR3, CCR5, iNOS, CD80, CD86, CD64, CD16 and CD32, CD68, and CD11 b is an antibody, a binding fragment thereof, an antibody-like molecule, or a binding fragment thereof.
  • the determination of a presence of the Th1- and/or M1 -dominant immune response is performed by contacting the sample with an agent that specifically binds to one or more of nucleic acids that encodes one or more proteins selected from protein selected from IgM, IgG, IgE, IFNy, TNFa, LTa, IL-17A, IL-6, IL-12, CXCR3, CCR5, iNOS, CD80, CD86, CD64, CD16 and CD32, CD68, and CD11 b.
  • the agent that specifically binds to one or more of the nucleic acids is a nucleic acid primer or probe.
  • the present disclosure relates to a method of determining treatment for a p53 mutant cancer in a patient, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method for selecting a patient having a p53 mutant cancer for a cancer treatment, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method for selecting a patient having a p53 mutant cancer for a cancer treatment, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of treating a p53 mutant cancer, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of determining treatment for a patient having higher activity of Tregs compared to effector T cells in the tumor microenvironment, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method for selecting for a cancer treatment a patient having higher activity of Tregs compared to effector T cells in the tumor microenvironment, the method comprising:
  • step (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of treating a cancer in a patient having higher activity of Tregs compared to effector T cells in the tumor microenvironment, the method comprising: (a) obtaining a biological sample from a subject; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is selected.
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is selected.
  • a lack of upregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation is observed compared to a prior biological sample obtained from the subject a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1, PD-L1 and/or PD-L2 is selected.
  • a cancer monotherapy when an upregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation is observed compared to a healthy tissue, a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1, PD-L1 and/or PD-L2 is not selected.
  • a chemotherapy is selected, the chemotherapy is selected from an antimetabolite chemotherapeutic (e.g., 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo- L-norleucine (DON), azaserine and acivicin), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc. ⁇ and a protein translation inhibitor (e.g., silvestrol and omacetaxine), a ribosome biogenesis inhibitor (e.g., diazaborine, lamotrigine and ribozinoindoles), an inhibitor of rRNA and/or tRNA synthesis (e.g., quarfloxin (CX-3543) and CX-5461), an inhibitor of synthesis of amino acids (e.g., GLUD1 inhibitor R162, BCAT1 inhibitor gaba
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is not selected.
  • a chemotherapy is selected, the chemotherapy is selected from an antimetabolite chemotherapeutic (e.g., 5- fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo-L-norleucine (DON), azaserine and acivicin), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc.); and a protein translation inhibitor (e.g., silvestrol and omacetaxine), a ribosome biogenesis inhibitor (e.g., diazaborine, lamotrigine and ribozinoindoles), an inhibitor of rRNA and/or tRNA synthesis (e.g., quarfloxin (CX-3543) and CX-5461), an inhibitor of synthesis of amino acids (e.g., GLUD1 inhibitor R162, BCAT1 inhibitor gaba
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is not selected.
  • a chemotherapy is selected, the chemotherapy is selected from an antimetabolite chemotherapeutic (e.g., 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo-L-norleucine (DON), azaserine and acivicin), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc.) and a protein translation inhibitor (e.g., silvestrol and omacetaxine), a ribosome biogenesis inhibitor (e.g., diazaborine, lamotrigine and ribozinoindoles), an inhibitor of rRNA and/or tRNA synthesis (e.g., quarfloxin (CX-3543) and CX-5461), an inhibitor of synthesis of amino acids (e.g., GLUD1 inhibitor R162, BCAT1 inhibitor gaba
  • the one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation is selected from Statl, Stat2, Tapi , Ifitm2, and Ifitm3.
  • the present disclosure relates to a method of determining treatment for a cancer in a subject that exhibits a potent NK-cell mediated cytotoxicity, a Th 1 - and/or M1-dominant immune response, and/or weak activity of CD4+CD25+T regulatory cells: (a) contacting a cultured biological sample from a subject with IFNy for less than about 8 hours; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method for selecting for a cancer treatment in a subject for cancer treatment, wherein the subject exhibits a potent NK-cell mediated cytotoxicity, a Th1 - and/or Mi- dominant immune response, and/or weak activity of CD4CD25+T regulatory cells, the method comprising: (a) contacting a cultured biological sample from a subject with IFNy for less than about 8 hours; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of treating a cancer in a subject that exhibits a potent NK-cell mediated cytotoxicity, a Th1- and/or M1 -dominant immune response, and/or weak activity of CD4+CD25+ T regulatory cells, the method comprising: (a) contacting a cultured biological sample from a subject with IFNy for less than about 8 hours; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the presence of the potent NK-cell mediated cytotoxicity is determined based on measurement of one or more of the proportion of NKP46+ cells, the proportion of NKP46+CD69+ cells, extent of CD107a surface expression, extent of cytokine production (e.g. production of one or more of IFNyJNFa, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1, CCL2, CCL3, CCL4, CCL5, and CXCL8), and extent of lysis of target cells.
  • cytokine production e.g. production of one or more of IFNyJNFa, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1, CCL2, CCL3, CCL4, CCL5, and CXCL8
  • the determination of a potent NK-cell mediated cytotoxicity is performed by DNA sequencing, RNA sequencing, immunohistochemical staining, western blotting, in cell western, immunofluorescent staining, ELISA, and fluorescent activating cell sorting (FACS) or a combination thereof.
  • the determination of a potent NK-cell mediated cytotoxicity is performed by contacting the sample with an agent that specifically binds to a protein selected from NKP46, CD69, IFNyJNFa, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1 , CCL2, CCL3, CCL4, CCL5, and CXCL8.
  • the agent that specifically binds to a protein selected from NKP46, CD69, IFNyJNFa, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1, CCL2, CCL3, CCL4, CCL5, and CXCL8 is an antibody, a binding fragment thereof, an antibody-like molecule, or a binding fragment thereof.
  • the determination of a potent NK-cell mediated cytotoxicity is performed by contacting the sample with an agent that specifically binds to one or more of nucleic acids that encodes one or more proteins selected from protein selected from NKP46, CD69, IFNy NFa, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1 , CCL2, CCL3, CCL4, CCL5, and CXCL8.
  • the agent that specifically binds to one or more of the nucleic acids is a nucleic acid primer or probe.
  • the presence of the Th1 - and/or M1-dominant immune response compared to a control is determined based on one or more of the ratios of IgM: IgG and/or IgEJgG antibodies, extent of cytokine production (e.g., production of one or more of IFNy, TNFa, LTa, IL-17A, IL-6, IL-12, CXCR3, CCR5), surface expression of one or more markers (e.g., iNOS, CD80, CD86, CD64, CD16 and CD32, along with CD68 and/or CD11 b).
  • cytokine production e.g., production of one or more of IFNy, TNFa, LTa, IL-17A, IL-6, IL-12, CXCR3, CCR5
  • markers e.g., iNOS, CD80, CD86, CD64, CD16 and CD32, along with CD68 and/or CD11 b).
  • the determination of a presence of the Th1- and/or M1-dominant immune response is performed by DNA sequencing, RNA sequencing, immunohistochemical staining, western blotting, in cell western, immunofluorescent staining, ELISA, and fluorescent activating cell sorting (FACS) or a combination thereof.
  • the determination of a presence of the Th1 - and/or M1-dominant immune response is performed by contacting the sample with an agent that specifically binds to a protein selected from IgM, IgG, IgE, IFNy, TNFa, LTa, IL-17A, IL-6, IL-12, CXCR3, CCR5, iNOS, CD80, CD86, CD64, CD16 and CD32, CD68, and CD11 b.
  • the agent that specifically binds to a protein selected from IgM, IgG, IgE, IFNy, TNFa, LTa, IL-17A, IL-6, IL-12, CXCR3, CCR5, iNOS, CD80, CD86, CD64, CD16 and CD32, CD68, and CD11 b is an antibody, a binding fragment thereof, an antibody-like molecule, or a binding fragment thereof.
  • the determination of a presence of the Th1- and/or M1 -dominant immune response is performed by contacting the sample with an agent that specifically binds to one or more of nucleic acids that encodes one or more proteins selected from protein selected from IgM, IgG, IgE, I FNy, TNFo, LTo, IL-17A, IL-6, IL-12, CXCR3, CCR5, iNOS, CD80, CD86, CD64, CD16 and CD32, CD68, and CD11 b.
  • the agent that specifically binds to one or more of the nucleic acids is a nucleic acid primer or probe.
  • the presence of the weak activity of CD4+CD25+ T regulatory cells compared to a control is determined based on one or more of the proportion of CD4+CD25+ T regulatory cells in peripheral blood, extent of cytokine production (e.g., production of IL-2, IL-10 and TGF ), proliferation assay.
  • the control is selected from a standard value or a sample from one or more normal subjects, subjects suffering from cancer, subjects suffering from cancer relapse, or a combination thereof.
  • the determination of a weak activity of CD4+CD25+ T regulatory cells is performed by DNA sequencing, RNA sequencing, immunohistochemical staining, western blotting, in cell western, immunofluorescent staining, ELISA, and fluorescent activating cell sorting (FACS) or a combination thereof.
  • the determination of a weak activity of CD4- D25+T regulatory cells is performed by contacting the sample with an agent that specifically binds to a protein selected from CD4, CD25, IL-2, IL-10 and TGF .
  • the agent that specifically binds to a protein selected from CD4, CD25, IL-2, IL-10 and TGF0 is an antibody, a binding fragment thereof, an antibody-like molecule, or a binding fragment thereof.
  • the determination of a weak activity of CD4-HDD25+T regulatory cells is performed by contacting the sample with an agent that specifically binds to one or more of nucleic acids that encodes one or more proteins selected from protein selected from CD4, CD25, IL-2, IL-10 and TGF .
  • the agent that specifically binds to one or more of the nucleic acids is a nucleic acid primer or probe.
  • the present disclosure relates to a method of determining treatment for a p53 mutant cancer in a patient, the method comprising: (a) contacting a cultured biological sample from a subject with IFNy for less than about 8 hours; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method for selecting a patient having a p53 mutant cancer for a cancer treatment, the method comprising: (a) contacting a cultured biological sample from a subject with IFNy for less than about 8 hours; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen process! ng/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • the present disclosure relates to a method of treating a p53 mutant cancer, the method comprising: (a) contacting a cultured biological sample from a subject with I FNy for less than about 8 hours; (b) evaluating the sample for the presence, absence, or level of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and (c) selecting a cancer therapy based on the evaluation of step (b).
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is selected.
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is selected.
  • an upregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation is observed compared to a prior biological sample obtained from the subject, a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1, PD-L1 and/or PD-L2 is selected.
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is not selected, wherein the therapy that is selected for administration is selected from an antimetabolite chemotherapeutic (e.g, 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo-L-norleucine (DON), azaserine and acivicin), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc.); and a protein translation inhibitor (e.g., silvestrol and omacetaxine), a ribosome biogenesis
  • an antimetabolite chemotherapeutic e.g, 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo-L-norleu
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1, PD-L1 and/or PD-L2 is not selected, wherein the therapy that is selected for administration is selected from an antimetabolite chemotherapeutic (e.g., 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo-L-norleucine (DON), azaserine and acivicin), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc.); and a protein translation inhibitor (e.g., silvestrol and o
  • an antimetabolite chemotherapeutic e.g., 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo-L-norleucine (DON), azaserine and
  • a cancer monotherapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is not selected, wherein the therapy that is selected for administration is selected from an antimetabolite chemotherapeutic (e.g., 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo-L-norleucine (DON), azaserine and acivicin), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc.); and a protein translation inhibitor (e.g., silvestrol and omacetaxine), a chemotherapeutic (e.g., 5-fluorouracil, methotrexate, capecitabine, azacitidine, 6-diazo-5-oxo-L-norleucine (DON), azaserine and
  • the one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation is selected from Statl, Stat2, Tapi, Ifitm2, and Ifitm3.
  • the cultured biological sample from a subject is contacted with an interferon for less than about 7 hr, or less than about 6 hr, or less than about 5 hr, or less than about 4 hr, or less than about 3 hr, or less than about 2 hr, or less than about 1 hr. In embodiments, the cultured biological sample from a subject is contacted with an interferon for at least about 5 minutes, or at least about 10 minutes, or at least about 15 minutes, or at least about 30 minutes, or at least about 45 hr, or at least about 1 hr, or at least about 2 hr, or at least about 3 hr, or at least about 4 hr.
  • the biological sample is a fresh tissue sample, frozen tumor tissue specimen, cultured cells, circulating tumor cells, or a formalin-fixed paraffin-embedded tumor tissue specimen.
  • the biological sample is a biopsy sample.
  • the biopsy sample is selected from endoscopic biopsy, bone marrow biopsy, endoscopic biopsy (e.g., cystoscopy, bronchoscopy, and colonoscopy), needle biopsy (e.g., fine-needle aspiration, core needle biopsy, vacuum-assisted biopsy, X-ray-assisted biopsy, computerized tomography (CT)-assisted biopsy, magnetic resonance imaging (MRI)-assisted biopsy and ultrasound-assisted biopsy), skin biopsy (e.g., shave biopsy, punch biopsy, and incisional biopsy) and surgical biopsy.
  • CT computerized tomography
  • MRI magnetic resonance imaging
  • the biological sample comprises a body fluid selected from blood, plasma, serum, lacrimal fluid, tears, bone marrow, blood, blood cells, ascites, tissue or fine needle biopsy sample, cell-containing body fluid, sputum, saliva, urine, cerebrospinal fluid, peritoneal fluid, pleural fluid, feces, lymph, gynecological fluid, skin swab, vaginal swab, oral swab, nasal swab, bone marrow specimen, tissue biopsy specimen, surgical specimen, feces, other body fluids, secretions, aspirate, scraping, and/or excretions and/or cells therefrom.
  • the biological sample comprises a washing or lavage selected from a ductal lavage or bronchoalveolar lavage, and/or cells therefrom.
  • the biological sample is obtained by a technique selected from scrapes, swabs, and biopsy.
  • the biological sample is obtained by use of brushes, (cotton) swabs, spatula, rinse/wash fluids, punch biopsy devices, puncture of cavities with needles or surgical instrumentation.
  • the biological sample comprises at least one tumor cell.
  • the tumor is selected from Hodgkin's and non-Hodgkin's lymphoma, B-cell lymphoma (including low grade/follicular nonHodgkin's lymphoma (NHL); small lymphocytic (SL) NHL; intermediate grade/follicular NHL; intermediate grade diffuse NHL; high grade immunoblastic NHL; high grade lymphoblastic NHL; high grade small noncleaved cell NHL; bulky disease NHL; mantle cell lymphoma; AIDS-related lymphoma; and Waldenstrom’s Macroglobulinemia; chronic lymphocytic leukemia (CLL); acute lymphoblastic leukemia (ALL); Hairy cell leukemia; or chronic myeloblastic leukemia, basal cell carcinoma, biliary tract cancer; bladder cancer; bone cancer; brain and central nervous system cancer; breast cancer; cancer of the peritoneum; cervical cancer; choriocarcinoma; colon and rectum cancer
  • NHL low grade
  • the evaluating is performed by DNA sequencing, RNA sequencing, immunohistochemical staining, western blotting, in cell western, immunofluorescent staining, ELISA, and fluorescent activating cell sorting (FACS) or a combination thereof.
  • the evaluating is performed by contacting the sample with an agent that specifically binds to one or more proteins involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation. In embodiments, the evaluating is performed by contacting the sample with an agent that specifically binds to one or more proteins induced by the Jak/Stat pathway. In embodiments, the evaluating is performed by contacting the sample with an agent that specifically binds to one or more proteins involved in interferon responsiveness. In embodiments, the evaluating is performed by contacting the sample with an agent that specifically binds to one or more proteins selected from Statl, Stat2, Tapi, Ifitm2, and Ifitm3.
  • the evaluating is performed by contacting the sample with an agent that specifically binds to one or more of nucleic acids that encodes one or more proteins involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation. In embodiments, the evaluating is performed by contacting the sample with an agent that specifically binds to one or more nucleic acid that encode one or more proteins induced by the Jak/Stat pathway. In embodiments, the evaluating is performed by contacting the sample with an agent that specifically binds to one or more nucleic acid that encode one or more proteins involved in interferon responsiveness.
  • the evaluating is performed by contacting the sample with an agent that specifically binds to one or more nucleic acid encoding one or more proteins selected from Statl , Stat2, Tapi , Ifitm2, and Ifitm3.
  • the agent that specifically binds to one or more of the nucleic acids is a nucleic acid primer or probe.
  • the evaluating informs classifying the patient into a high or low risk group.
  • the high-risk classification comprises a high level of tumor cells having resistance to the cancer therapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2.
  • low risk classification comprises a low level of tumor cells having resistance to the cancer therapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2.
  • the low risk or high- risk classification is indicative of withholding of a neoadjuvant therapy.
  • the low risk or high- risk classification is indicative of withholding of an adjuvant therapy.
  • the evaluating is predictive of a positive response to and/or benefit from the cancer treatment. In embodiments, the evaluating is predictive of a negative or neutral response to and/or benefit from the cancer treatment. In embodiments, the evaluating is predictive of a positive response to and/or benefit from neoadjuvant chemotherapy or a nonresponsiveness to and/or lack of benefit from neoadjuvant chemotherapy. In embodiments, the evaluating is predictive of a positive response to and/or benefit from adjuvant chemotherapy or a non-responsiveness to and/or lack of benefit from adjuvant chemotherapy.
  • the evaluating is predictive of a negative or neutral response to and/or benefit from neoadjuvant chemotherapy or a non-responsiveness to and/or lack of benefit from neoadjuvant chemotherapy. In embodiments, the evaluating is predictive of a negative or neutral response to and/or benefit from adjuvant chemotherapy or a non-responsiveness to and/or lack of benefit from adjuvant chemotherapy. In embodiments, the evaluating informs administration or withholding of the cancer treatment. In embodiments, the evaluating informs administration of neoadjuvant therapy. In embodiments, the evaluating informs administration of adjuvant therapy. In embodiments, the evaluating informs withholding of neoadjuvant therapy. In embodiments, the evaluating informs withholding of adjuvant therapy.
  • the neoadjuvant therapy and/or the adjuvant therapy is selected from a chemotherapeutic agent, a cytotoxic agent, a checkpoint inhibitor, an antimetabolite chemotherapeutic (e.g., 5-fluorouracil, methotrexate, capecitabine, azacitidine), a topoisomerase inhibitor (e.g., irinotecan, topotecan, etoposide, doxorubicin, etc.).
  • the neoadjuvant therapy and/or the adjuvant therapy is selected from a protein translation inhibitor (e. g .
  • a modulator of assembly and/or function of ribosomal complex a modulator of expression and/or function of tRNA, a modulator of synthesis and/or uptake of amino acids, a modulator of post-translational modification (e.g., decoration of the translated protein with carbohydrates), a modulator of protein degradation, and a modulator of protein transport (e.g., post-translational peptide processing, signal peptide recognition and cleavage, transport through the ER/Golgi network, etc.), etc.) or topoisomerase inhibitors.
  • a modulator of assembly and/or function of ribosomal complex a modulator of expression and/or function of tRNA, a modulator of synthesis and/or uptake of amino acids, a modulator of post-translational modification (e.g., decoration of the translated protein with carbohydrates), a modulator of protein degradation, and a modulator of protein transport (e.g., post-translational peptide processing, signal peptide
  • the neoadjuvant therapy and/or the adjuvant therapy is selected from a protein translation inhibitor (e.g., silvestrol and omacetaxine) ribosome biogenesis inhibitors (e.g., diazaborine, lamotrigine and ribozinoindoles), inhibitors of rRNA and/or tRNA synthesis (e.g., quarfloxin (CX- 3543) and CX-5461), an inhibitor of synthesis of amino acids (e.g., GLUD1 inhibitor R162, BCAT1 inhibitor gabapentin, glutaminase inhibitor bis-2-(5-phenylacetamido-1 ,2,4-thiadiazol-2-yl)ethyl sulfide (BPTES), PAGDH inhibitor NCT-503), an inhibitor of uptake of amino acids (e.g., SLC7A11 inhibitors sulfasalazine, erastin or sorafenib), a protein translation inhibitor
  • the present disclosure relates to a transgenic non-human animal comprising one or more tumor cells, wherein the tumor cells exhibit: (a) an upregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and/or (b) a lack of significant upregulation and/or a downregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation, when contacted with IFNy for less than about 8 hours.
  • the tumor cells are resistant to a cancer therapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2.
  • the cancer therapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2 is an antibody.
  • the antibody is a human or humanized antibody.
  • the antibody is selected from nivolumab (OPDIVO), pembrolizumab (KEYTRUDA), pidilizumab (CT-011, CURE TECH), MK-3475 (MERCK), BMS 936559, MPDL328OA (ROCHE), Cemiplimab (LIBTAYO), Atezolizumab (TECENTRIQ), Avelumab (BAVENCIO), and Durvalumab (imfinzi).
  • OPDIVO nivolumab
  • KEYTRUDA pembrolizumab
  • pidilizumab CT-011, CURE TECH
  • MK-3475 MK-3475
  • BMS 936559 MPDL328OA
  • ROCHE Cemiplimab
  • LIBTAYO Cemiplimab
  • Atezolizumab TECENTRIQ
  • Avelumab BAVENCIO
  • Durvalumab imfinzi
  • the one or more tumor cells exhibit: (a) an upregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and/or (b) a lack of significant upregulation and/or a downregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation, when contacted with IFNy for less than about 8 hours.
  • the one or more tumor cells demonstrate an upregulation of one or more proteins involved in interferon responsiveness.
  • the one or more tumor cells demonstrate an upregulation of one or more genes associated with cellular response to IFNy.
  • the transgenic non-human animal is a rodent.
  • the rodent is a mouse.
  • the mouse belongs to BALB/c or C57BL/6 strain.
  • the one or more cancer cells are colorectal carcinoma cells. In embodiments, the one or more cancer cells are p53 mutant and/or SMAD4 mutant and/or Kras+. In embodiments, the one or more cancer cells are derived from MC38 cells or a derivative thereof.
  • the present disclosure relates to a method of making a transgenic non-human animal comprising one or more p53 mutant cancer cells that are nonresponsive, resistant, or recalcitrance to a cancer therapy, wherein the cancer therapy has an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2, the method comprising: (a) injecting one or more parental p53 mutant cancer cells that are responsive to the cancer therapy in a non-human animal; (b) administering the cancer therapy to the non-human animal; (c) isolating cancer cells that survive the cancer therapy; (d) injecting cancer cells that survive the cancer therapy in a different non-human animal of the same species; and (e) repeating steps (b) to (d) three to ten more times.
  • a transgenic non-human animal comprising one or more p53 mutant cancer cells that are nonresponsive, resistant, or recalcitrance to a cancer therapy, wherein the non-human animal exhibits a potent NK-cell mediated cytotoxicity, a Th1 - and/or M1-dominant immune response, and/or weak activity of CD4- ⁇ D25+ T regulatory cells, and wherein the cancer therapy has an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2, the method comprising: (a) injecting one or more parental p53 mutant cancer cells that are responsive to the cancer therapy in a non-human animal; (b) administering the cancer therapy to the non-human animal; (c) isolating cancer cells that survive the cancer therapy; (d) injecting cancer cells that survive the cancer therapy in a different non-human animal of the same species; and (e) repeating steps (b) to (d) three to ten more times.
  • steps (b) to (d) are repeated at least three times more. In embodiments, steps (b) to (d) are repeated at least four times more. In embodiments, steps (b) to (d) are repeated at least five times more. In embodiments, steps (b) to (d) are repeated less than eight times.
  • the cancer cells that survive the cancer therapy grow faster than the parental p53 mutant cancer cells in the presence of the cancer therapy that has an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2.
  • the transgenic non-human animal is a rodent.
  • the rodent is a mouse.
  • the mouse belongs to BALB/c or C57BL/6 strain.
  • the one or more p53 mutant cancer cells are colorectal carcinoma cells. In embodiments, the one or more p53 mutant cancer cells are SMAD4 mutant and/or Kras+. In embodiments, the one or more cancer cells are derived from MC38 cells or a derivative thereof.
  • the cancer therapy that has the ability reduce or inhibit function and/or activity of PD-1 , PD- L1 and/or PD-L2 is an antibody.
  • the antibody is a human or humanized antibody. In embodiments, the antibody is a human or humanized antibody.
  • the antibody is selected from nivolumab (OPDIVO), pembrolizumab (KEYTRUDA), pidilizumab (CT-011 , CURE TECH), MK-3475 (MERCK), BMS 936559, MPDL328OA (ROCHE), Cemiplimab (LIBTAYO), Atezolizumab (TECENTRIQ), Avelumab (BAVENCIO), and Durvalumab (imfinzi).
  • the cancer therapy is capable of inhibiting the growth of tumor when administered to a transgenic non-human animal transgenic non-human animal harboring a parental cancer cell tumor compared to an untreated transgenic non-human animal harboring a parental cancer cell tumor.
  • the tumor cells that survive the cancer therapy exhibit: (a) an upregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation; and/or (b) a lack of significant upregulation and/or a downregulation of one or more genes involved in interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation, when contacted with IFNy for less than about 8 hours.
  • the one or more tumor cells demonstrate an upregulation of one or more genes associated with cellular response to IFNy and/or type I IFN signaling pathway.
  • the present disclosure relates to a transgenic animal made according to the method of any of the embodiments disclosed herein.
  • the transgenic non-human animal can be any animal that is known to be useful for mimicking the human cancer.
  • the transgenic non-human animal may be a pig, cow, dog, cat, horse, donkey, goat, sheep, llama, or non-human primate (e.g., chimpanzee).
  • the transgenic non-human animal is a mammal.
  • the transgenic non-human animal may be a rodent, such as a rat, mouse, hamster, rabbit, or guinea pig.
  • the transgenic non-human animal is a mouse.
  • the transgenic non-human animal is a rat.
  • the mouse belongs to BALB/c or C57BL/6 strain. Such mice can be purchased from different suppliers, e.g., from Charles River Laboratories.
  • the transgenic non-human animal is a transgenic non-human animal (without limitation, e.g., a transgenic mouse).
  • the transgenic non-human animal is a transgenic mouse.
  • the transgenic mouse has a heterozygous mutation in Trp53 gene.
  • the formation of tumor in the transgenic non-human animal is caused by a gene knock-out of one or more genes, optionally, the gene knock-out of one or more genes is inducible.
  • the knock-out of one or more genes carried out using cre-loxP, CRISPR/Cas9, or the like, or a combination thereof.
  • the knock-out of one or more genes is associated with an upregulation of one or more genes in the cells that have the knock-out of one or more genes.
  • the knock-out of one or more genes is associated with a downregulation of one or more genes in the cells that have knock-out of one or more genes.
  • the upregulation and the downregulation of one or more genes are independently optionally inducible.
  • the upregulation and/or the downregulation is caused by placing one or more sequences (without limitation, e.g., an RNAi construct, a Cre recombinase construct and a gene knock-in construct) under the control of a promoter that controls expression of one or more genes.
  • the transgenic non-human animal e.g., mouse
  • the transgenic non-human animal has mutations that will cause rampant chromosomal instability.
  • Such cancer-prone non-human animals are disclosed by Artandi et al., Telomere dysfunction promotes nonreciprocal translocations and epithelial cancers in mice, Nature 2000; 406(6796): 641-645; Zhu et al., Unrepaired DNA breaks in p53-deficient cells lead to oncogenic gene amplification subsequent to translocations, Cell 2002; 109(7): 811-821 ; Olive et al., Mutant p53 Gain of Function in Two Mouse Models of Li-Fraumeni Syndrome, Ce//2004;119(6): 847-860; Lang et al., Gain of function of a p53 hot spot mutation in a mouse model of Li-Fraumeni syndrome, Ce// 2004; 119(6): 861-872; and
  • Transgenic non-human animal e.g., mouse
  • the formation of tumor in the transgenic non-human animal is caused by a knock-in of one or more tumor-causing-genes, optionally, the knock-in of one or more tumor-causing-genes is inducible.
  • tumor-causing-genes are well-known in the art, and in embodiments include known oncogenes selected from c-Myc, HRAS G12V or Kras G12D and dominant negative p53 mutants.
  • the knock-in of one or more tumor-causing-genes carried out using cre-loxP, CRISPR/Cas9, or the like, or a combination thereof.
  • the knock-in of one or more tumor-causing-genes is associated with an upregulation of one or more genes in the cells that have the knock-in of one or more tumor-causing-genes. In embodiments, the knock-in of one or more tumor-causing-genes is associated with a downregulation of one or more genes in the cells that have knock-in of one or more tumor-causing-genes. In embodiments, the upregulation and the downregulation of one or more genes are independently optionally inducible.
  • the upregulation and/or the downregulation is caused by placing one or more sequences (without limitation, e.g., an RNAi construct, a Cre recombinase construct and a further gene knock-in construct) under the control of a promoter that controls expression of one or more genes.
  • one or more sequences without limitation, e.g., an RNAi construct, a Cre recombinase construct and a further gene knock-in construct
  • the formation of tumor in the transgenic non-human animal is caused by a chromosomal translocation, optionally, the chromosomal translocation is inducible.
  • the chromosomal translocation carried out using cre-loxP, CRISPR/Cas9, or the like, or a combination thereof.
  • the chromosomal translocation is associated with an upregulation of one or more genes in the cells that have the chromosomal translocation.
  • the chromosomal translocation is associated with a downregulation of one or more genes in the cells that have chromosomal translocation.
  • the upregulation and the downregulation of one or more genes are independently optionally inducible.
  • the upregulation and/or the downregulation is caused by placing one or more sequences (without limitation, e.g., an RNAi construct, a Cre recombinase construct and a gene knock-in construct) under the control of a promoter that controls expression of one or more genes.
  • one or more sequences without limitation, e.g., an RNAi construct, a Cre recombinase construct and a gene knock-in construct
  • the formation of tumor in the transgenic non-human animal is caused by a chromosomal inversion, optionally, the chromosomal inversion is inducible.
  • the chromosomal inversion carried out using cre-loxP, CRISPR/Cas9, or the like, or a combination thereof.
  • the chromosomal inversion is associated with an upregulation of one or more genes in the cells that have the chromosomal inversion.
  • the chromosomal inversion is associated with a downregulation of one or more genes in the cells that have chromosomal inversion.
  • the upregulation and the downregulation of one or more genes are independently optionally inducible.
  • the upregulation and/or the downregulation is caused by placing one or more sequences (without limitation, e.g., an RNAi construct, a Cre recombinase construct and a gene knock-in construct) under the control of a promoter that controls expression of one or more genes.
  • one or more sequences without limitation, e.g., an RNAi construct, a Cre recombinase construct and a gene knock-in construct
  • the present disclosure relates to a method for testing an anti-cancer drug candidate, the method comprising: (a) providing a transgenic non-human animal of any of the embodiments disclosed herein, or a transgenic non-human animal made according to the method of any of the embodiments disclosed herein;
  • the present disclosure relates to a method for making a pharmaceutical composition for treating cancer, the method comprising: (a) providing a transgenic non-human animal of any of the embodiments disclosed herein or a transgenic non-human animal made according to the method of any of the embodiments disclosed herein; (b) administering the anti-cancer drug candidate to the transgenic non-human animal, and
  • the anti-cancer drug candidate is selected from a chemotherapeutic agent, a cytotoxic agent, and a checkpoint inhibitor.
  • the cancer therapy (and/or additional agents) described herein can possess a sufficiently basic functional group, which can react with an inorganic or organic acid, or a carboxyl group, which can react with an inorganic or organic base, to form a pharmaceutically acceptable salt.
  • a pharmaceutically acceptable acid addition salt is formed from a pharmaceutically acceptable acid, as is well known in the art.
  • Such salts include the pharmaceutically acceptable salts listed in, for example, Journal of Pharmaceutical Science, 66, 2-19 (1977) and The Handbook of Pharmaceutical Salts; Properties, Selection, and Use. P. H. Stahl and C. G. Wermuth (eds.), Verlag, Zurich (Switzerland) 2002, which are hereby incorporated by reference in their entirety.
  • compositions described herein are in the form of a pharmaceutically acceptable salt.
  • any cancer therapy (and/or additional agents) described herein can be administered to a subject as a component of a composition that comprises a pharmaceutically acceptable carrier or vehicle.
  • Such compositions can optionally comprise a suitable amount of a pharmaceutically acceptable excipient so as to provide the form for proper administration.
  • Pharmaceutical excipients can be liquids, such as water and oils, including those of petroleum, animal, vegetable, or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like.
  • the pharmaceutical excipients can be, for example, saline, gum acacia, gelatin, starch paste, talc, keratin, colloidal silica, urea and the like.
  • the pharmaceutically acceptable excipients are sterile when administered to a subject.
  • Water is a useful excipient when any agent described herein is administered intravenously.
  • Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid excipients, specifically for injectable solutions.
  • Suitable pharmaceutical excipients also include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. Any agent described herein, if desired, can also comprise minor amounts of wetting or emulsifying agents, or pH buffering agents.
  • compositions described herein are resuspended in a saline buffer (including, without limitation TBS, PBS, and the like).
  • a saline buffer including, without limitation TBS, PBS, and the like.
  • the present disclosure includes the described cancer therapy (and/or additional agents) in various formulations.
  • Any cancer therapy (and/or additional agents) described herein can take the form of solutions, suspensions, emulsion, drops, tablets, pills, pellets, capsules, capsules containing liquids, powders, sustained-release formulations, suppositories, emulsions, aerosols, sprays, suspensions, or any other form suitable for use.
  • DNA or RNA constructs encoding the protein sequences may also be used.
  • the composition is in the form of a capsule (see, e.g., U.S. Patent No. 5,698,155).
  • suitable pharmaceutical excipients are described in Remington’s Pharmaceutical Sciences 1447-1676 (Alfonso R.
  • the formulations comprising the cancer therapy (and/or additional agents) can also include a solubilizing agent.
  • the agents can be delivered with a suitable vehicle or delivery device as known in the art.
  • Combination therapies outlined herein can be co-delivered in a single delivery vehicle or delivery device.
  • Compositions for administration can optionally include a local anesthetic such as, for example, lignocaine to lessen pain at the site of the injection.
  • the formulations comprising the cancer therapy (and/or additional agents) of the present disclosure may conveniently be presented in unit dosage forms and may be prepared by any of the methods well known in the art of pharmacy. Such methods generally include the step of bringing therapeutic agents into association with a carrier, which constitutes one or more accessory ingredients. Typically, the formulations are prepared by uniformly and intimately bringing therapeutic agent into association with a liquid carrier, a finely divided solid carrier, or both, and then, if necessary, shaping the product into dosage forms of the desired formulation (e.g., wet or dry granulation, powder blends, etc., followed by tableting using conventional methods known in the art)
  • a carrier which constitutes one or more accessory ingredients.
  • the formulations are prepared by uniformly and intimately bringing therapeutic agent into association with a liquid carrier, a finely divided solid carrier, or both, and then, if necessary, shaping the product into dosage forms of the desired formulation (e.g., wet or dry granulation, powder blends, etc., followed by tableting using conventional methods known
  • any cancer therapy (and/or additional agents) described herein is formulated in accordance with routine procedures as a composition adapted for a mode of administration described herein.
  • Routes of administration include, for example: intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, oral, sublingual, intranasal, intracerebral, intravaginal, transdermal, rectally, by inhalation, or topically, particularly to the ears, nose, eyes, or skin.
  • the administering is effected orally or by parenteral injection. In most instances, administration results in the release of any agent described herein into the bloodstream.
  • cancer therapy can be administered orally.
  • Such cancer therapy (and/or additional agents) can also be administered by any other convenient route, for example, by intravenous infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, etc.) and can be administered together with another biologically active agent. Administration can be systemic or local.
  • Various delivery systems are known, e.g., encapsulation in liposomes, microparticles, microcapsules, capsules, etc., and can be used to administer.
  • the cancer therapy (and/or additional agents) are administered in the tumor microenvironment (e.g., cells, molecules, extracellular matrix and/or blood vessels that surround and/or feed a tumor cell, inclusive of, for example, tumor vasculature; tumor-infiltrating lymphocytes; fibroblast reticular cells; endothelial progenitor cells (EPC); cancer-associated fibroblasts; pericytes; other stromal cells; components of the extracellular matrix (ECM); dendritic cells; antigen presenting cells; T-cells; regulatory T cells; macrophages; neutrophils; and other immune cells located proximal to a tumor) or lymph node and/or targeted to the tumor microenvironment or lymph node.
  • the cancer therapy (and/or additional agents) are administered intratumorally.
  • Dosage forms suitable for parenteral administration include, for example, solutions, suspensions, dispersions, emulsions, and the like. They may also be manufactured in the form of sterile solid compositions (e.g., lyophilized composition), which can be dissolved or suspended in sterile injectable medium immediately before use. They may contain, for example, suspending or dispersing agents known in the art.
  • any cancer therapy (and/or additional agents) described herein as well as the dosing schedule can depend on various parameters, including, but not limited to, the disease being treated, the subject’s general health, and the administering physician’s discretion.
  • Any cancer therapy described herein can be administered prior to (e.g., 5 minutes, 15 minutes, 30 minutes, 45 minutes, 1 hour, 2 hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 hours, 72 hours, 96 hours, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 8 weeks, or 12 weeks before), concurrently with, or subsequent to (e.g., 5 minutes, 15 minutes, 30 minutes, 45 minutes, 1 hour, 2 hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 hours, 72 hours, 96 hours, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 8 weeks, or 12 weeks after) the administration of an additional agent, to a subject in need thereof.
  • any cancer therapy and additional agent described herein are administered 1 minute apart, 10 minutes apart, 30 minutes apart, less than 1 hour apart, 1 hour apart, 1 hour to 2 hours apart, 2 hours to 3 hours apart, 3 hours to 4 hours apart, 4 hours to 5 hours apart, 5 hours to 6 hours apart, 6 hours to 7 hours apart, 7 hours to 8 hours apart, 8 hours to 9 hours apart, 9 hours to 10 hours apart, 10 hours to 11 hours apart, 11 hours to 12 hours apart, 1 day apart, 2 days apart, 3 days apart, 4 days apart, 5 days apart, 6 days apart, 1 week apart, 2 weeks apart, 3 weeks apart, or 4 weeks apart.
  • any cancer therapy (and/or additional agents) described herein can depend on several factors including the severity of the condition, whether the condition is to be treated or prevented, and the age, weight, and health of the subject to be treated. Additionally, pharmacogenomic (the effect of genotype on the pharmacokinetic, pharmacodynamic or efficacy profile of a therapeutic) information about a particular subject may affect dosage used. Furthermore, the exact individual dosages can be adjusted somewhat depending on a variety of factors, including the specific combination of the agents being administered, the time of administration, the route of administration, the nature of the formulation, the rate of excretion, the particular disease being treated, the severity of the disorder, and the anatomical location of the disorder. Some variations in the dosage can be expected.
  • the dosage may be about 0.1 mg to about 250 mg per day, about 1 mg to about 20 mg per day, or about 3 mg to about 5 mg per day.
  • the dosage of any agent described herein may be about 0.1 mg to about 1500 mg per day, or about 0.5 mg to about 10 mg per day, or about 0.5 mg to about 5 mg per day, or about 200 to about 1,200 mg per day (e.g., about 200 mg, about 300 mg, about 400 mg, about 500 mg, about 600 mg, about 700 mg, about 800 mg, about 900 mg, about 1 ,000 mg, about 1 ,100 mg, about 1,200 mg per day).
  • administration of the cancer therapy (and/or additional agents) described herein is by parenteral injection at a dosage of about 0.1 mg to about 1500 mg per treatment, or about 0.5 mg to about 10 mg per treatment, or about 0.5 mg to about 5 mg per treatment, or about 200 to about 1 ,200 mg per treatment (e.g., about 200 mg, about 300 mg, about 400 mg, about 500 mg, about 600 mg, about 700 mg, about 800 mg, about 900 mg, about 1 ,000 mg, about 1 ,100 mg, about 1 ,200 mg per treatment).
  • a suitable dosage of the cancer therapy is in a range of about 0.01 mg/kg to about 100 mg/kg of body weight ,or about 0.01 mg/kg to about 10 mg/kg of body weight of the subject, for example, about 0.01 mg/kg, about 0.02 mg/kg, about 0.03 mg/kg, about 0.04 mg/kg, about 0.05 mg/kg, about 0.06 mg/kg, about 0.07 mg/kg, about 0.08 mg/kg, about 0.09 mg/kg, about 0.1 mg/kg, about 0.2 mg/kg, about 0.3 mg/kg, about 0.4 mg/kg, about 0.5 mg/kg, about 0.6 mg/kg, about 0.7 mg/kg, about 0.8 mg/kg, about 0.9 mg/kg, about 1 mg/kg, about 1 .1 mg/kg, about 1 .2 mg/kg, about 1.3 mg/kg, about 1 .4 mg/kg, about 1.5 mg/kg, about 1.6 mg/kg, about 1.7 mg/kg, about 1.8 mg
  • delivery can be in a vesicle, in particular a liposome (see Langer, 1990, Science 249:1527-1533; Treat et al., in Liposomes in therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989).
  • Any cancer therapy (and/or additional agents) described herein can be administered by controlled-release or sustained-release means or by delivery devices that are well known to those of ordinary skill in the art. Examples include, but are not limited to, those described in U.S. Patent Nos.
  • Such dosage forms can be useful for providing controlled- or sustained-release of one or more active ingredients using, for example, hydropropylmethyl cellulose, other polymer matrices, gels, permeable membranes, osmotic systems, multilayer coatings, microparticles, liposomes, microspheres, or a combination thereof to provide the desired release profile in varying proportions.
  • Controlled- or sustained-release of an active ingredient can be stimulated by various conditions, including but not limited to, changes in pH, changes in temperature, stimulation by an appropriate wavelength of light, concentration or availability of enzymes, concentration or availability of water, or other physiological conditions or compounds.
  • polymeric materials can be used (see Medical Applications of Controlled Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Florida (1974); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball (eds.), Wiley, New York (1984); Ranger and Peppas, 1983, J. Macromol. Sci. Rev. Macromol. Chem. 23:61 ; see also Levy et al., 1985, Science 228:190; During et al., 1989, Ann. Neurol. 25:351; Howard et al., 1989, J. Neurosurg. 71 :105).
  • a controlled-release system can be placed in proximity of the target area to be treated, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115-138 (1984)).
  • Other controlled-release systems discussed in the review by Langer, 1990, Science 249:1527-1533 may be used.
  • Administration of any cancer therapy (and/or additional agents) described herein can, independently, be one to four times daily or one to four times per month or one to six times per year or once every two, three, four or five years. Administration can be for the duration of one day or one month, two months, three months, six months, one year, two years, three years, and may even be for the life of the subject.
  • the dosage regimen utilizing any cancer therapy (and/or additional agents) described herein can be selected in accordance with a variety of factors including type, species, age, weight, sex and medical condition of the subject; the severity of the condition to be treated; the route of administration; the renal or hepatic function of the subject; the pharmacogenomic makeup of the individual; and the specific compound of the invention employed.
  • Any cancer therapy (and/or additional agents) described herein can be administered in a single daily dose, or the total daily dosage can be administered in divided doses of two, three or four times daily.
  • any cancer therapy (and/or additional agents) described herein can be administered continuously rather than intermittently throughout the dosage regimen.
  • the phrase “potent NK-cell mediated cytotoxicity” in a subject means that the extent of cytotoxic activity of NK cells in the subject is more than average cytotoxic activity of NK cells in control subjects.
  • the control subjects may be normal subjects, subjects suffering from cancer, subjects suffering from cancer relapse, or a combination thereof.
  • the extent of cytotoxic activity of NK cells in the subject may be measured using an appropriate assay including, but not limited to, an assay measuring the proportion of NKP46+ cells in peripheral blood, the proportion of NKP46+CD69+ cells in peripheral blood, extent of CD107a surface expression, extent of cytokine production (e.g., production of IFNy NFo, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1 , CCL2, CCL3, CCL4, CCL5, and CXCL8), extent of ability to induce lysis of target cells, and a combination thereof.
  • an assay measuring the proportion of NKP46+ cells in peripheral blood, the proportion of NKP46+CD69+ cells in peripheral blood, extent of CD107a surface expression, extent of cytokine production (e.g., production of IFNy NFo, granulocyte macrophage colony-stimulating factor (GM-CSF), CCL1 , CCL2, CCL3, CCL4, CCL5,
  • the appropriate assays include, e.g., assays that use one or more agents that specifically binds to one or more proteins expressed by NK cells and/or one or more agents that specifically binds to nucleic acid encoding one or more proteins expressed by NK cells (e.g., one or more ELISA-based, a flowcytometry-based, a RT-PCR-based, a real-time cell electronic sensing (RT-CES) system-based assay).
  • agents that specifically binds to one or more proteins expressed by NK cells e.g., one or more ELISA-based, a flowcytometry-based, a RT-PCR-based, a real-time cell electronic sensing (RT-CES) system-based assay.
  • RT-CES real-time cell electronic sensing
  • Somanchi et al. A Novel Method for Assessment of Natural Killer Cell Cytotoxicity Using Image Cytometry, PLoS One 2015; 10(10): e0141074; Park et al., Evaluation of NK Cell Function by Flowcytometric Measurement and Impedance Based Assay Using Real-Time Cell Electronic Sensing System, Biomed Res Int. 2013; 2013: 210726.
  • the term “weak activity of CD4+CD25+ T regulatory cells” in a subject means that the extent of activity of CD4- 3D25+ T regulatory cells in the subject is more than average activity of CD4-H3D25+ T regulatory cells in control subjects.
  • the control subjects may be normal subjects, subjects suffering from cancer, subjects suffering from cancer relapse, or a combination thereof.
  • the activity of CD4+CD25+ T regulatory cells compared to a control may be measured using an appropriate assay including, but not limited to, an assay measuring the proportion of CD4+CD25+T regulatory cells in peripheral blood, extent of cytokine production (e.g., production of IL-2, IL-10 and TGF
  • the appropriate assays include, e.g., assays that use one or more agents that specifically binds to one or more proteins expressed by NK cells and/or one or more agents that specifically binds to nucleic acid encoding one or more proteins expressed by NK cells (e.g., one or more ELISA-based, a flowcytometry-based, a RT-PCR-based). Antony and Restifo CD4-HDD25+ T Regulatory Cells, Immunotherapy of Cancer, and lnterleukin-2, J Immunother.
  • the examples herein are provided to illustrate advantages and benefits of the present disclosure and to further assist a person of ordinary skill in the art with preparing or using cells that are resistant to anti-PD-1 , anti-PD-L1 and/or anti-PD-L2 therapy.
  • the examples herein are also presented in order to more fully illustrate the preferred aspects of the present disclosure.
  • the examples should in no way be construed as limiting the scope of the present disclosure, as defined by the appended claims.
  • the examples can include or incorporate any of the variations, aspects or embodiments of the present disclosure described above.
  • the variations, aspects or embodiments described above may also further each include or incorporate the variations of any or all other variations, aspects or embodiments of the present disclosure.
  • Murine colorectal carcinoma MC38 cell were subjected to selection for surviving the anti-PD-1 treatment to generate anti-PD-1- antibody resistant MC38 cells.
  • the method used to generation of the anti-PD-1 -resistant MC38 tumor cells is illustrated in FIG. 1A. Briefly, wild-type (WT) MC38 colorectal carcinoma cells were acquired from the National Cancer Institute (NCI), and were cultured in IMDM media, with 10% FBS, antibiotic/antimycotic, and gentamycin (all GIBCO), in an incubator at 37 °C with 5% CO2. Cell lines in active culture were tested monthly using the VENOR GEM Mycoplasma Detection Kit (Sigma).
  • 500,000 MC38 cells were inoculated on the hind flank of C57BL/6 mice (Jackson Laboratories), and when tumors became palpable, mice where either treated with vehicle (PBS) or anti-PD-1 (100 mg of clone RMP1- 14 on days 0, 3, and 6 via intraperitoneal injection (IP); BioXCell). Tumor growth was measured over time and after approximately 20 days following the first treatment, tumors from anti-PD-1 -treated mice were isolated (indicating round 1), dissociated using collagenase (StemCell Technologies), washed in 1 x PBS, and plated in culture media (1 st round MC38/AR cells), these cells were passaged a minimum of 2 times and were then used to inoculate new C57BL/6 mice.
  • PBS vehicle
  • anti-PD-1 100 mg of clone RMP1- 14 on days 0, 3, and 6 via intraperitoneal injection (IP); BioXCell.
  • tumor measurements were taken over time, and tumors were isolated approximately 20 days after treatment, from anti-PD-1-non-responding animals (indicating round 2; 2 nd round MC38/AR cells).
  • This in vivo anti-PD-1 selective pressure was performed for a total of 5 rounds until none of the mice responded to anti-PD-1 therapy.
  • These isolated tumors are referred to as ‘5 th round’ and represent the tumors cells used to characterize the MC38 CPI acquired resistance model (MC38/AR) (FIG. 1A).
  • mice were inoculated in rear flanks with MC38 parental cells or MC38/AR cells obtained after 3, 4 or 5 rounds of selection.
  • STV starting tumor volume
  • mice harboring treatments were initiated.
  • Half of the mice harboring MC38 parental cell tumors were treated with vehicle only control on days 0, 3, and 6.
  • mice harboring MC38 parental cell tumors and mice harboring tumors of MC38/AR cells after 3, 4 or 5 rounds of selection (3 rd , 4 th or 5 th round MC38/AR cells) were given a series of intraperitoneal injections of 100 pg anti-PD-1 (clone RMP1-14; BioXcell) on days 0, 3, and 6. Tumor volumes were measured on day 20 and plotted.
  • FIG. 1 B the growth of MC38 parental cell tumors in mice treated with the anti-PD-1 antibody was retarded to about 43% compared to the growth of MC38 parental cell tumors in mice that were treated with vehicle only control. This response was in line with a typically observed response to anti-PD-1 therapy.
  • Example 2 Analysis of Expression of Genes Associated with Interferon Responsiveness, Jak/Stat Signaling, and Antigen Processing/Presentation in Response to Interferon Gamma in Resistant Cells PD-1 Resistant Cells
  • genes associated with interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation including Statl , Stat2, Tapi, Ifitm2, and Ifitm3, was studied in the 5 th round MC38/AR cells compared to the parental MC38 cells.
  • cDNA was diluted further with nuclease-free water and qPCR was performed at a series of genes, in triplicate, and SYBR Green signal was assessed on the BioRad CFX Opus 96 and CFX Touch 96.
  • Mouse validated gene primer sequences from Origene were used, and included mouse Statl, Stat2, Tapi , Ifitm2, Ifitm3, and the house-keeping control Rps18. Fold-change in gene expression at baseline was calculated using the ddCT method where the first WT tumor sample was set to 1 . Each additional gene was compared to this sample and the Rps18 house-keeping control. The results are shown in FIG. 2A to FIG. 2E.
  • MC38/AR cells showed an increased expression of Statl (FIG. 2A), Stat2 (FIG. 2B), Tapi (FIG. 2C), Ifitm2 (FIG. 2D), and Ifitm3 (FIG. 2E).
  • Example 3 Dysregulation of Genes Associated with Interferon Responsiveness, Jak/Stat Signaling, and Antigen Processing/Presentation in Response to Interferon Gamma in Resistant Cells PD-1 Resistant Cells in Response to Interferon Gamma Stimulation
  • I FNy interferon gamma
  • cDNA was diluted further with nuclease-free water and qPCR was performed at a series of genes, in triplicate, and SYBR Green signal was assessed on the BioRad CFX Opus 96 and CFX Touch 96.
  • Mouse validated gene primer sequences from Origene were used, and included mouse Statl , Stat2, Tapi , Ifitm2, Ifitm3, and the house-keeping control Rps18. Fold-change in IFNy responsiveness was calculated using the ddCT method where each IFNy treated tumor samples was normalized to its representative IFNy untreated samples. The results are shown in FIG. 3A to FIG. 3E.
  • MC38/AR cells showed a decreased expression of Statl (FIG. 3A), Stat2 (FIG. 3B), Tapi (FIG. 3C), and Ifitm3 (FIG. 3E). Ifitm2 showed a very modest increase in expression upon IFNy treatment in MC38/AR cells compared to MC38 parental cells (FIG. 3D).
  • IFNy-responsiveness e.g., a lack of overexpression
  • genes associated with interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation including Statl, Stat2, Tapi , Ifitm2, and Ifitm3 in a p53 mutant cancer, indicates a development of resistance, a lack of response, or recalcitrance to the cancer therapy with an ability to reduce or inhibit function and/or activity of PD-1 , PD-L1 and/or PD-L2.
  • IFNy-responsiveness e.g., overexpression
  • genes associated with interferon responsiveness, Jak/Stat signaling, and antigen processing/presentation including Statl , Stat2, Tapi , Ifitm2, and Ifitm3 in a p53 mutant cancer, indicates sensitivity to the cancer therapy with an ability to reduce or inhibit function and/or activity of PD-1, PD-L1 and/or PD-L2.

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Immunology (AREA)
  • Cell Biology (AREA)
  • Engineering & Computer Science (AREA)
  • Hematology (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Urology & Nephrology (AREA)
  • Biomedical Technology (AREA)
  • Oncology (AREA)
  • Medicinal Chemistry (AREA)
  • Animal Behavior & Ethology (AREA)
  • Microbiology (AREA)
  • General Physics & Mathematics (AREA)
  • Biotechnology (AREA)
  • Veterinary Medicine (AREA)
  • Public Health (AREA)
  • Environmental Sciences (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Food Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • Hospice & Palliative Care (AREA)
  • Pathology (AREA)
  • Zoology (AREA)
  • Animal Husbandry (AREA)
  • Biodiversity & Conservation Biology (AREA)
  • Epidemiology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Organic Chemistry (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)

Abstract

La présente divulgation concerne des modèles animaux, des méthodes de criblage et de test d'un médicament anticancéreux candidat, ainsi que des méthodes de traitement, d'évaluation de l'efficacité d'un traitement anticancéreux et de sélection de patients pour une cancérothérapie.
PCT/US2023/079476 2022-11-14 2023-11-13 Méthodes permettant de surmonter la résistance à des thérapies par inhibiteur de point de contrôle WO2024107624A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202263425085P 2022-11-14 2022-11-14
US63/425,085 2022-11-14

Publications (1)

Publication Number Publication Date
WO2024107624A1 true WO2024107624A1 (fr) 2024-05-23

Family

ID=91085321

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2023/079476 WO2024107624A1 (fr) 2022-11-14 2023-11-13 Méthodes permettant de surmonter la résistance à des thérapies par inhibiteur de point de contrôle

Country Status (1)

Country Link
WO (1) WO2024107624A1 (fr)

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20140314814A1 (en) * 2011-10-20 2014-10-23 California Stem Cell, Inc. Antigen presenting cancer vaccine
US20170261508A1 (en) * 2014-03-14 2017-09-14 The Trustees Of The University Of Pennsylvania Methods for monitoring cd4+ t-helper type 1 response in cancer and immune restoration
WO2018225062A1 (fr) * 2017-06-04 2018-12-13 Rappaport Family Institute For Research In The Medical Sciences Procédé de prédiction de réponse personnalisée à une thérapie anticancéreuse et kit associé
US20220339249A1 (en) * 2019-09-25 2022-10-27 Bristol-Myers Squibb Company Composite biomarker for cancer therapy

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20140314814A1 (en) * 2011-10-20 2014-10-23 California Stem Cell, Inc. Antigen presenting cancer vaccine
US20170261508A1 (en) * 2014-03-14 2017-09-14 The Trustees Of The University Of Pennsylvania Methods for monitoring cd4+ t-helper type 1 response in cancer and immune restoration
WO2018225062A1 (fr) * 2017-06-04 2018-12-13 Rappaport Family Institute For Research In The Medical Sciences Procédé de prédiction de réponse personnalisée à une thérapie anticancéreuse et kit associé
US20220339249A1 (en) * 2019-09-25 2022-10-27 Bristol-Myers Squibb Company Composite biomarker for cancer therapy

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
KATANO MITSUO, WADA JUNJI; YAMASAKI AKIO; NAGAI SHUNTARO; YANAI KOUSUKE; FUCHINO KOUTA; KAMEDA CHIZU; TANAKA HARUO; KOGA KENICHIRO: "Regulatory T-Cells Are Possible Effect Prediction Markers of Immunotherapy for Cancer Patients", ANTICANCER RESEARCH, vol. 28, 1 August 2008 (2008-08-01), pages 2401 - 2408, XP093174552 *
PICARD EMILIE, GODET YANN; LAHEURTE CAROLINE; DOSSET MAGALIE; GALAINE JEANNE; BEZIAUD LAURENT; LOYON ROMAIN; BOULLEROT LAURA; LAUR: "Circulating NKp46 + Natural Killer cells have a potential regulatory property and predict distinct survival in Non-Small Cell Lung Cancer", ONCOIMMUNOLOGY, vol. 8, no. 2, 1 February 2019 (2019-02-01), pages e1527498, XP093174550, ISSN: 2162-402X, DOI: 10.1080/2162402X.2018.1527498 *
TATSUMI TOMOHIDE ET AL: "Disease-associated bias in T helper type 1 (Th1)/Th2 CD4+ T cell responses against MAGE-6 in HLA-DRB1*0401+ patients with renal cell carcinoma or melanoma", JOURNAL OF EXPERIMENTAL MEDICINE, ROCKEFELLER UNIVERSITY PRESS, US, vol. 196, no. 5, 2 September 2002 (2002-09-02), US , pages 619 - 628, XP002309752, ISSN: 0022-1007, DOI: 10.1084/jem.20012142 *

Similar Documents

Publication Publication Date Title
JP7458188B2 (ja) 腫瘍を処置する方法
AU2017315459B2 (en) Methods of treating fibroblast growth factor 19-mediated cancers and tumors
US20240190963A1 (en) Methods of treating tumor
US10023649B2 (en) Method of treating cancer with a combination of an anti-CCR4 antibody and a 4-1BB agonist
EP3498734B1 (fr) Combinaison d'un antagoniste pd-1 et d'un inhibiteur vegfr pour le traitement du cancer
US20210025895A1 (en) Cancer serum biomarkers and methods of use thereof
JP2020536894A (ja) 腫瘍処置法
JP2023182572A (ja) がんの診断及び治療方法
KR20250020678A (ko) 암을 치료하기 위한 pd-1 길항제 및 vegfr/fgfr/ret 티로신 키나제 억제제의 조합
AU2015360736A1 (en) System and methods for deriving gene signature biomarkers of response to PD-1 antagonists
WO2016059220A1 (fr) Agents d'activation du tcr à utiliser dans le traitement de la lla-t
US20230088070A1 (en) Use of il-1beta binding antibodies
TW201900193A (zh) 用於癌症治療之生物標記物
US20240011101A1 (en) Method of determining resistance to checkpoint inhibitor therapies
JP2019527037A (ja) がんのための診断及び治療方法
CN117321418A (zh) 癌症生物标志物及其使用方法
EP4104856A1 (fr) Utilisation d'anticorps anti-pd-1 dans le traitement de tumeurs
TW202231283A (zh) 用於治療轉移性大腸直腸癌之經改良之基於氟尿嘧啶之多藥劑化學治療
WO2024107624A1 (fr) Méthodes permettant de surmonter la résistance à des thérapies par inhibiteur de point de contrôle
WO2023039249A1 (fr) Polythérapie
CN116829953A (zh) 确定对检查点抑制剂疗法的抗性的方法
KR20200061382A (ko) 암을 치료하기 위한 조성물 및 방법

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 23892342

Country of ref document: EP

Kind code of ref document: A1

点击 这是indexloc提供的php浏览器服务，不要输入任何密码和下载